The aim of this work is to develop a new estuarine classification attending to their vertical structure by examining the advantages and disadvantages of the existing classifications. For this purpose, we reviewed the main classifications, finding that most of them analyze the entire estuary as a unique water body without considering the spatiotemporal variability of the mixing zone in estuaries. Furthermore, the proposed classifications require the calculation of parameters that are not easily measurable, such as tidal current amplitude. Thus, we developed a new classification based on density profile slopes of the water column, which has been correlated to the potential energy anomaly. To test this classification, the proposed method was applied to the Suances estuary (Spain) during the year 2020 and to analyze the potential estuarine modifications under four climate change projections (RCP 4.5 and 8.5 for the years 2050 and 2100). To carry out this study, a calibrated and validated high-resolution horizontal and vertical 3D model was used. The application showed a high variability in the vertical structure of the estuary due to the tide and river. According to the proposed classification, the well mixed category was predominant in the estuary in 2020 and tended to grow in the projections of climate change. As a result, the fully mixed and weakly stratified mixing classes were reduced in the projected scenarios due to a decrease of external forcing, such as river flow and sea level rise. Furthermore, areas classified as stratified tended to move upstream of the estuary.